Some things to consider. Direct flights to Bonaire can be expensive but if you fly into Curacao or Aruba and grab an island hopper across the cost can be a lot less. I just returned from Bonaire, direct flights were anywhere from $1200 to $1500, god knows why, I got a flight into Curacao for $570 and an island hopper across for $130 ($30 of which was departure tax) for a total of $700. I just did a quick check of DFW/CUR, it was right at $600, odds are that price will drop to mid to low $500s if you watch. Point is, airfare can be less if you are willing to do some transfers. It's a little bit of a PITA but not bad.
Most rooms on Bonaire are condos. If you are so inclined, you can cook breakfast and/or lunch to save quite a bit of cash. That option may or may not be available other places. This can make up for a good bit of airfare.
The other issue is how much diving do you want to get in. If you are doing just 2 a day and relaxing the rest of the time then other places with cheaper air may be the way to go but if you want 4 or more dives a day then at most places, that will require more boat cost which will very quickly override the extra airfare to Bonaire.
You will often hear people talk about how expensive Bonaire is compared to other places, I find the complete opposite to be true if you fairly compare what you are getting. A simple X cost $2000 and Y cost $3000 so X is cheaper is not a good comparison. The way I rate the cost of a dive location is $ per minute of bottom time, the vast majority of the time Bonaire wins hands down for me. I simply add the total cost of the trip, food, air, diving, room and anything else and divide that by the total minutes of bottom time I get. My average on Bonaire is 4 dives per day at 75 minutes per dive. On boat only trips to places like Coz, that drops to 2 dives at 45 minutes per dive. The extra dive and extended bottom time add up quickly. Value increases a lot if you add in intangibles like not having to deal with a herd of divers or ending a dive with 1500 psi due to a air hog on board.